Omics Biology in Diagnosis of Diseases: Advances in Bioinformatics and Data Analyses

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: 28 June 2024 | Viewed by 5997

Special Issue Editors


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Guest Editor
CICS – Health Sciences Research Center, Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal
Interests: bioinformatics and computational biology; omics; comparative genomics; evolutionary genomics; precision medicine; human genetics; clinical genomics; WGS; WES
Institute of Biotechnology, University of Helsinki, Helsinki, Finland
Interests: comparative genomics; metagenomics; transcriptomics; single-cell RNA-seq; evo-devo

Special Issue Information

Dear Colleagues,

The study and diagnosis of many human diseases is often difficult due to a number of factors. Diseases have diverse causes, such as, for instance, interactions with the environment, food habits, microbiome and/or genetics. Specifically, in this latter case, we are chiefly concerned with hereditary genetics, in particular with the identification of the causes that induce the symptoms presented by the patients. Here, the physician often requires the collection of samples, something which will allow the performance of the genetics diagnosis. These samples often undergo the process of sequencing (i.e., whole-exome sequencing—WES) which enables the detection of deleterious genetic changes and other variation found in the protein-coding regions of the human genome. However, the genetic causes may also be located outside of the coding regions, i.e., in noncoding DNA, which comprises more than 90% of the human genome. Here, the whole-genome sequencing (WGS) methods become necessary. Additionally, GWAS, epigenomics, transcriptomics, and other omics can reveal themselves to be useful in the study and molecular diagnosis of human diseases.

Moreover, several bioinformatics advances have enabled the analysis of data originating from these sequencing technologies and often benefit from tools and methods previously developed in the context of evolutionary and comparative genomics.

This issue of Life invites authors to publish original research on all aspects of i) genome biology and ii) human molecular disease diagnosis (WES, WGS, etc), with preference for articles in the former, demonstrating the (potential of) application to the latter. Potential areas for consideration include: 1) bioinformatics software and methods, possibly incorporating evolutionary and/or comparative omics aspects; 2) analyses of cohorts suspected of rare genetics diseases considering the identification of its causes; 3) omics analyses involving the human and/or other evolutionarily close species; and 4) manuscripts considering the analyses of human microbiome (pathogens) or other factors with potential to influence the human genetics and/or cause disease.

Dr. Emanuel Maldonado
Dr. Imran Khan
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bioinformatics
  • software and methods
  • clinical genomics
  • mendelian diseases
  • evolutionary and comparative genomics
  • whole-exome sequencing
  • next-/third-generation sequencing
  • whole-genome sequencing
  • multi-omics
  • microbiome diseases

Published Papers (4 papers)

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Research

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14 pages, 2265 KiB  
Article
Structural and Dynamic Analyses of Pathogenic Variants in PIK3R1 Reveal a Shared Mechanism Associated among Cancer, Undergrowth, and Overgrowth Syndromes
by Nikita R. Dsouza, Catherine E. Cottrell, Olivia M. T. Davies, Megha M. Tollefson, Ilona J. Frieden, Donald Basel, Raul Urrutia, Beth A. Drolet and Michael T. Zimmermann
Life 2024, 14(3), 297; https://doi.org/10.3390/life14030297 - 23 Feb 2024
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Abstract
The PI3K enzymes modify phospholipids to regulate cell growth and differentiation. Somatic variants in PI3K are recurrent in cancer and drive a proliferative phenotype. Somatic mosaicism of PIK3R1 and PIK3CA are associated with vascular anomalies and overgrowth syndromes. Germline PIK3R1 variants are associated [...] Read more.
The PI3K enzymes modify phospholipids to regulate cell growth and differentiation. Somatic variants in PI3K are recurrent in cancer and drive a proliferative phenotype. Somatic mosaicism of PIK3R1 and PIK3CA are associated with vascular anomalies and overgrowth syndromes. Germline PIK3R1 variants are associated with varying phenotypes, including immunodeficiency or facial dysmorphism with growth delay, lipoatrophy, and insulin resistance associated with SHORT syndrome. There has been limited study of the molecular mechanism to unify our understanding of how variants in PIK3R1 drive both undergrowth and overgrowth phenotypes. Thus, we compiled genomic variants from cancer and rare vascular anomalies and sought to interpret their effects using an unbiased physics-based simulation approach for the protein complex. We applied molecular dynamics simulations to mechanistically understand how genetic variants affect PIK3R1 and its interactions with PIK3CA. Notably, iSH2 genetic variants associated with undergrowth destabilize molecular interactions with the PIK3CA receptor binding domain in simulations, which is expected to decrease activity. On the other hand, overgrowth and cancer variants lead to loss of inhibitory interactions in simulations, which is expected to increase activity. We find that all disease variants display dysfunctions on either structural characteristics or intermolecular interaction energy. Thus, this comprehensive characterization of novel mosaic somatic variants associated with two opposing phenotypes has mechanistic importance and biomedical relevance and may aid in future therapeutic developments. Full article
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14 pages, 24966 KiB  
Article
Network Proteins of Human Sortilin1, Its Expression and Targetability Using Lycopene
by Arun H. S. Kumar
Life 2024, 14(1), 137; https://doi.org/10.3390/life14010137 - 18 Jan 2024
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Abstract
Background: Sortilin1 (SORT1) is a ubiquitously expressed transporter involved in sorting or clearing proteins and is pathologically linked to tissue fibrosis and calcification. Targeting SORT1 may have potential clinical efficacy in controlling or reversing cardiovascular fibrosis and/or calcification. Hence, this study assessed the [...] Read more.
Background: Sortilin1 (SORT1) is a ubiquitously expressed transporter involved in sorting or clearing proteins and is pathologically linked to tissue fibrosis and calcification. Targeting SORT1 may have potential clinical efficacy in controlling or reversing cardiovascular fibrosis and/or calcification. Hence, this study assessed the protein–protein network of human SORT1 and its targetability using known nutra-/pharmaceuticals. Material and methods: Network proteins of human SORT1 were identified using the String database, and the affinity of the protein–protein interaction of this network was analysed using Chimera software (Chimera-1.17.3-mac64). The tissue-specific expression profile of SORT1 was evaluated and assessed for enrichment in different cell types, including immune cells. A library of in-house small molecules and currently used therapeutics for cardiovascular diseases were screened using AutoDock Vina to assess the targetability of human SORT1. The concentration affinity (CA) ratio of the small molecules was estimated to assess the clinical feasibility of targeting SORT1. Results: IGF2R, NTRK2, GRN and GGA1 were identified as high-affinity interaction networks of SORT1. Of these high-affinity interactions, IGF2R and GRN can be considered relevant networks in regulating tissue fibrosis or the microcalcification process due to their influence on T-cell activation, inflammation, wound repair, and the tissue remodelling process. The tissue cell-type enrichment indicated major expression of SORT1 in adipocytes, specialised epithelial cells, monocytes, cardiomyocytes, and thyroid glandular cells. The binding pocket analysis of human SORT1 showed twelve potential drug interaction sites with varying binding scores (0.86 to 5.83) and probability of interaction (0.004 to 0.304). Five of the drug interaction sites were observed to be targetable at the therapeutically feasible concentration of the small molecules evaluated. Empagliflozin, sitagliptin and lycopene showed a superior affinity and CA ratio compared to established inhibitors of SORT1. Conclusion: IGF2R and GRN are relevant networks of SORT1, regulating tissue fibrosis or the microcalcification process. SORT1 can be targeted using currently approved small-molecule therapeutics (empagliflozin and sitagliptin) or widely used nutraceuticals (lycopene), which should be evaluated in a randomised clinical trial to assess their efficacy in reducing the cardiac/vascular microcalcification process. Full article
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16 pages, 6464 KiB  
Article
Novel LDLR Variant in Familial Hypercholesterolemia: NGS-Based Identification, In Silico Characterization, and Pharmacogenetic Insights
by Mohammad Athar, Mawaddah Toonsi, Zainularifeen Abduljaleel, Abdellatif Bouazzaoui, Neda M. Bogari, Anas Dannoun and Faisal A. Al-Allaf
Life 2023, 13(7), 1542; https://doi.org/10.3390/life13071542 - 11 Jul 2023
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Abstract
Background: Familial Hypercholesterolemia (FH) is a hereditary condition that causes a rise in blood cholesterol throughout a person’s life. FH can result in myocardial infarction and even sudden death if not treated. FH is thought to be caused mainly by variants in the [...] Read more.
Background: Familial Hypercholesterolemia (FH) is a hereditary condition that causes a rise in blood cholesterol throughout a person’s life. FH can result in myocardial infarction and even sudden death if not treated. FH is thought to be caused mainly by variants in the gene for the low-density lipoprotein receptor (LDLR). This study aimed to investigate the genetic variants in FH patients, verify their pathogenicity, and comprehend the relationships between genotype and phenotype. Also, review studies assessed the relationship between the LDLR null variants and the reaction to lipid-lowering therapy. Methods: The study utilised high-throughput next-generation sequencing for genetic screening of FH-associated genes and capillary sequencing for cascade screening. Furthermore, bioinformatic analysis was employed to describe the pathogenic effects of the revealed novel variant on the structural features of the corresponding RNA molecule. Results: We studied the clinical signs of hypercholesterolemia in a Saudi family with three generations of FH. We discovered a novel frameshift variant (c.666_670dup, p.(Asp224Alafs*43) in the LDLR and a known single nucleotide variant (c.9835A > G, p.(Ser3279Gly) in the APOB gene. It is thought that the LDLR variant causes a protein to be prematurely truncated, likely through nonsense-mediated protein decay. The LDLR variant is strongly predicted to be pathogenic in accordance with ACMG guidelines and co-segregated with the FH clinical characteristics of the family. This LDLR variant exhibited severe clinical FH phenotypes and was restricted to the LDLR protein’s ligand-binding domain. According to computational functional characterization, this LDLR variant was predicted to change the free energy dynamics of the RNA molecule, thereby affecting its stability. This frameshift variant is thought to eliminate important functional domains in LDLR that are required for receptor recycling and LDL particle binding. We provide insight into how FH patients with a null variant in the LDLR gene respond to lipid-lowering therapy. Conclusions: The findings expand the range of FH variants and assist coronary artery disease preventive efforts by improving diagnosis, understanding the genotype-phenotype relationship, prognosis, and personalised therapy for patients with FH. Full article
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Review

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12 pages, 567 KiB  
Review
Mechanisms of Epigenetic Inheritance in Post-Traumatic Stress Disorder
by Pei-Chen Chou, Yu-Chi Huang and Sebastian Yu
Life 2024, 14(1), 98; https://doi.org/10.3390/life14010098 - 08 Jan 2024
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Abstract
Post-traumatic stress disorder (PTSD) is a psychiatric disorder that causes debilitating functional impairment in patients. Observations from survivors of traumatic historical events solidify that this disease is not only associated with personal experiences but can also be inherited from familial traumas. Over the [...] Read more.
Post-traumatic stress disorder (PTSD) is a psychiatric disorder that causes debilitating functional impairment in patients. Observations from survivors of traumatic historical events solidify that this disease is not only associated with personal experiences but can also be inherited from familial traumas. Over the past decades, researchers have focused on epigenetic inheritance to understand how responses to adverse experiences can be passed down to future generations. This review aims to present recent findings on epigenetic markers related to PTSD and research in the intergenerational inheritance of trauma. By understanding the information, we hope that epigenetic markers can act as biochemical measurements for future clinical practice. Full article
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